US9982312B2 - Microbial assay - Google Patents

Microbial assay Download PDF

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US9982312B2
US9982312B2 US13/516,600 US201013516600A US9982312B2 US 9982312 B2 US9982312 B2 US 9982312B2 US 201013516600 A US201013516600 A US 201013516600A US 9982312 B2 US9982312 B2 US 9982312B2
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nucleic acid
acid sequence
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David Pearce
Mark Enright
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Binx Health Ltd
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Definitions

  • the present invention relates to assay products, uses and methods, especially those involving the Polymerase Chain Reaction (PCR). More specifically it relates to assays for Chlamydia trachomatis and to improved controls for PCR.
  • PCR Polymerase Chain Reaction
  • Chlamydia trachomatis is an obligate intracellular human pathogen. Chlamydia infection is a common sexually-transmitted disease and the bacterium can cause numerous disease states in both men and women. Clinical symptoms include urethritis, proctitis, trachoma, infertility, prostatitis, epididymitis, cervicitis, pelvic inflammatory disease (PID) and ectopic pregnancy. It is also a neonatal pathogen where it can cause infection of the eyes and lungs.
  • Chlamydia trachomatis Infection with Chlamydia trachomatis is one of the most common sexually transmitted diseases worldwide. It is estimated that 2-3 million individuals in the United States are infected with Chlamydia . In the United Kingdom, it has been estimated that one in ten sexually active young people under 25 are infected with Chlamydia.
  • Chlamydia trachomatis infection can be successfully treated by antibiotics, for example, tetracyclines such as doxycycline or acrolides such as azithromycin.
  • antibiotics for example, tetracyclines such as doxycycline or acrolides such as azithromycin.
  • tetracyclines such as doxycycline or acrolides such as azithromycin.
  • a national programme of Chlamydia screening has been launched.
  • the infectious unit of Chlamydia trachomatis is the elementary body (EB).
  • the EB functions as a “spore-like” body whose purpose is to permit Chlamydial survival in a non-supportive environment outside of the host cell.
  • the EB is thought to be metabolically inert until it attaches to and is endocytosed by a susceptible host cell.
  • Detection of Chlamydia trachomatis is possible by nucleic acid amplification methods, for example, Polymerase Chain Reaction (PCR) based methods. PCR has the potential to amplify nucleic acid from both infected cells and EBs.
  • PCR Polymerase Chain Reaction
  • Chlamydia trachomatis contains genetic material in both its chromosome, which is present as a single copy, and in its plasmid which is present in, 6 to 10 copies per EB.
  • the plasmid has been used as a preferred target for nucleic acid amplification tests due to its multiple copies per EB and the assumed greater sensitivity obtainable by detecting a plasmid-based target.
  • suitability of the plasmid nucleic acid amplification test detection systems has been called into question following the discovery of the Swedish variant of Chlamydia trachomatis .
  • the Swedish variant contains a 377 base pair deletion in the plasmid and therefore detection systems targeted at the deleted region will give a false negative result when confronted with Swedish variant Chlamydia trachomatis.
  • the present invention is based on the realisation that an assay detecting sequence present in the Chlamydia trachomatis chromosome is potentially more stable because the chromosomal genes are in general less mutable and because in certain circumstances it may be possible for the plasmid to be lost entirely.
  • Targeting a gene present in the chromosome might be expected to be disadvantageous because chromosomal targets are only present as a single copy per cell.
  • the inventors of the present invention were surprised to discover that chromosomal targets are able to provide limits of detection (LOD) comparable to plasmid targets.
  • LOD limits of detection
  • NAATs Nucleic Acid Amplification Tests
  • NAAT nucleic acid amplification test
  • LCR ligase chain reaction
  • SDA strand displacement amplification
  • RPA recombinase-polymerase amplification
  • NASBA nucleic acid sequence-based amplification
  • HNAAT methods have largely displaced culture based detection for C. trachomatis methods not least because culture based methods involved the added complexity of requiring the use of mammalian cell or tissue culture. They involve detecting nucleic acids in a highly sensitive sequence-specific manner involving amplification of one or more target sequences using enzymes.
  • PCR is a method of detecting nucleic acids in a highly sensitive sequence-specific manner involving amplification of one or more target sequences by using a thermostable polymerase enzyme and cycling the temperature conditions of the reaction.
  • a PCR reaction cycles through three stages: i) a denaturation stage occurring at a temperature of approximately 90-100° C. At this elevated temperature double-stranded DNA denatures or “melts” to form single-stranded DNA, ii) primer annealing at a typical temperature of 50-65° C. In this step the forward and reverse primers hybridize to the complimentary regions of any target present in the solution, and iii) extension typically occurring at 50-80° C. during which the polymerase chain reaction utilises deoxynucleotide triphosphates in the solution to extend the 3′ end of the primers. Typically, the cycle is carried out 25-45 times.
  • the annealing step and the extension step may be conflated so that the sample cycles through a two-step programme of 90° C. to 100° C. then 50° C. to 80° C. intervals.
  • Theoretical calculations show that a 30 cycle PCR reaction can amplify a single target molecule 268,435,456 times. Because of inefficiencies in the amplification reaction, actual amplification may be less than this, but nevertheless the PCR reaction is typically able to amplify single or very low numbers of target molecules millions of times to a level at which they can be much more easily detected.
  • PCR reactions rely on a thermostable DNA polymerase, for example, Taq polymerase isolated from the thermophilic bacterium Thermus aquaticus . Other thermostable DNA polymerases can be used in place of Taq, for example, Pfu polymerase isolated from Pyrococcus furiosus which has a proof-reading activity absent from Taq polymerase and is therefore a higher fidelity enzyme.
  • the detection of amplified PCR products may be carried out in a non-specific way which merely detects the presence of double-stranded nucleic acid (for example, by use of a double-stranded-DNA intercalating dye such as ethidium bromide or SYBR-green).
  • a semi-specific detection of product may be carried out by resolving approximate molecular weight of the product, for example, by Carrying out an electrophoresis of the reaction products prior to detection.
  • sequence-specific detection methods typically involve the hybridization of a sequence-specific nucleic acid probe to the amplified region or which measure the degradation of the probe concomitant with the amplification of the target sequence and make use of the nucleic acid exonuclease activity of the nucleic acid polymerase.
  • PCR-based methods of detection for pathogenic agents typically offer the advantage of faster results than more traditional methods which usually involve culture and incubation over a number of days. A PCR result can be made available in a few hours or less.
  • a method of detecting in a sample genetic material deriving from Chlamydia trachomatis comprising sequence-specific detection of a nucleic acid sequence, said nucleic acid sequence comprising at least 10 contiguous nucleotide residues contained in SEQ ID NO: 1
  • a forward PCR primer comprising a nucleic acid sequence comprising between 17 and 34 contiguous nucleotide residues selected from SEQ ID NO: 15
  • SEQ ID NO: 15 tgatg - g/c-t/a-t/a-t/a-g/c -g/c-a/t- cactagtc agcatcaagc taggagatt
  • sequence of the primer deriving from SEQ ID NO: 15 may be shorter (preferably between 12 and 22 or 19 and 29 residues in length) if steps are taken to increase the annealing temperature of the primer.
  • a reverse PCR primer comprising a nucleic acid sequence comprising, between 15 and 31 contiguous nucleotide residues selected from SEQ ID NO: 16
  • SEQ ID NO: 16 aaggaagatt ccagaggcaa tgccaaagaa aaaagt
  • sequence of the primer deriving from SEQ ID NO: 16 may be shorter (preferably between 10 and 20 or 16 and 26 residues in length) if steps are taken to increase the annealing temperature of the primer.
  • nucleic acid probe comprising a nucleic acid sequence, said nucleic acid sequence comprising between 18 and 28 nucleic acid residues given in SEQ ID NO: 4
  • sequence of the probe deriving from SEQ ID NO: 4 may be shorter (preferably between 13 and 23 residues in length) if steps are taken to increase the annealing temperature of the probe.
  • a PCR component comprising a forward PCR primer according to the invention and a reverse PCR primer according to the invention.
  • kits comprising a PCR component as according to the invention and instructions for carrying out a method according to the invention.
  • a seventh aspect of the invention there is provided a method of detecting in a sample genetic material deriving from Pectobacterium atrosepticum comprising sequence-specific detection of a nucleic acid sequence, contained in the chromosome of Pectobacterium atrosepticum.
  • forward PCR primers as defined as a “second forward PCR primer” in accordance with the fifth aspect of the invention
  • reverse PCR primer as defined as a “second reverse PCR primer” in accordance with the fifth aspect of the invention
  • PCR probe as defined as a “second PCR probe” in accordance with the fifth aspect of the invention.
  • the invention also provides PCR components comprising any one or more forward PCR primer, reverse PCR primer or PCR probe in accordance with the eighth, ninth or tenth aspect of the invention in combination with one or more further components of a PCR reaction.
  • FIGS. 1 a to 1 c show the results of Limit of Detection (LOD) determination experiments carried out for plasmid target amplicons 3, 5 and 7 as described in the examples.
  • LOD Limit of Detection
  • FIGS. 2 a to 2 c show the results of Limit of Detection (LOD) determination experiments carried out for chromosomic target amplicons 9, 17 and 18 as described in the examples.
  • LOD Limit of Detection
  • FIG. 2 d shows the results of the chromosomal amplicon 17 [Mg 2+ ] optimisation experiment as described in the examples.
  • FIG. 3 shows the results of the chromosomal amplicon 17 experiments described in example 8.
  • the legend for each bar within each group of 4 is as in FIG. 5 .
  • the legend “ME17 primers+20 pg IC DNA” corresponds to the first bar in each group of 4.
  • the legend “ME17 primers, no IC DNA” refers to the second bar in each group of four.
  • the legend “ME17 and IC primers+200 ⁇ g IC DNA” refers to the third bar in each group of four.
  • the legend “ME17 and IC primers; no IC DNA” refers to the fourth bar in each group of four.
  • FIG. 5 as FIG. 4 , but for experiment carried out to detect internal control amplicons.
  • FIG. 6 a shows an electrophoretic gel of amplification products of Chlamydia trachomatis without the Internal Control primer set.
  • Lane 1 100 bp ladder
  • lanes 2 to 4 10,000 IFU reactions
  • lanes 5 to 7 1,000 IFU reactions
  • lanes 8 to 10 100 IFU reactions
  • lanes 11 to 13 10 IFU reactions
  • lanes 14 to 16 1 IFU reaction.
  • FIG. 7 a and FIG. 7 b as FIGS. 6 a and 6 b but for reactions containing the Internal Control primer set.
  • FIG. 9 shows the results of the comparative duplex experiments described in Example 10.
  • PCR is a technique widely used in molecular biology to amplify a segment of DNA by in vitro enzymatic replication. As the reaction progresses, the DNA generated by earlier replications are used as templates for later replications. This sets in motion a chain reaction in which DNA template is exponentially or approximately exponentially amplified. With PCR it is possible to amplify single or very few copies of nucleic acid across several orders of magnitude generating a Million or more copies which May be more easily detected.
  • the basic PCR set-up requires the following components: i) a DNA template or target to be amplified; ii) a pair of primer's; the forward primer which is complementary to the DNA region at the 5′ prime end of the target region and the reverse primer which is complementary to the DNA region at the 3′ prime end of the target region; iii) a thermostable DNA polymerase, for example, Taq polymerase; iv) deoxynucleoside triphosphates (dNTPs). These are used as the building blocks from which the DNA polymerase synthesises the new DNA strand; v) a suitable buffer solution; vi) magnesium ions or other suitable cations; vii) monovalent potassium ions or other suitable cations.
  • multiplex PCR involves the simultaneous amplification of more than one target in a single sample container.
  • Multiplex PCR includes duplex and triplex PCR reactions involving up to a dozen sets of primers acting independently.
  • Nested PCR is a technique which can be used to increase specificity of a PCR amplification reaction.
  • Two sets of primers are used in two successive reactions. In the first one a pair of primers is used to generate DNA products in a less than completely specific fashion. Nevertheless, the first reaction increases the instance of the target sequence. The second reaction is more specific and amplifies a sequence nested within the first set of primers.
  • Quantitative PCR is used to measure or estimate the specific amount of target DNA in a sample.
  • the normal PCR process may, under some circumstances, be approximately quantitative but the aim of true quantitative PCR is to run the amplification reaction or consider the results of the amplification reaction only within the phase of true exponential increase of product amount, thereby avoiding the later plateau phase of amplification.
  • the amount of product in the exponential phase of amplification is much more proportional to the initial amount of target.
  • Thermocyclers have been developed which can monitor the amount of product during amplification.
  • One method currently used is quantitative real-time PCR which uses a fluorescent dye such as SYBR-green or fluorophore-containing DNA probes such as the proprietary TaqManTM system to measure the amount of amplified product as the amplification progresses.
  • Hot-start PCR avoids a possible problem whereby the primers are able to bind at low temperatures to non-specific locations or even to each other.
  • Hot-start PCR is based on the principle of releasing the primers for hybridization only when the reaction temperature is sufficiently high to prevent or reduce non-specific primer binding.
  • the technique can be performed manually by heating the reaction components to the denaturation temperature, for example 94° C. before adding the polymerase or before adding the primers.
  • specialised systems have been developed which inhibit the reaction until the temperature is raised by, for example, binding one or more of the components in an inactive form to be released on the raising of temperature.
  • Reverse transcriptase PCR is a method used to amplify RNA in which a PCR reaction is preceded by a reaction using reverse transcriptase to convert RNA to cDNA. The two reactions are sufficiently compatible that they can be run in the same tube and be carried out in the same thermal cycling instrument.
  • Methylation-specific PCR or involves pre-treating the target DNA with sodium bisulphite which converts unmethylated cytosine units into uracil which is recognised by the DNA primers as thymine.
  • Two amplifications are carried out on the modified DNA using primer sets which distinguish between the modified and unmodified templates.
  • One primer set recognises DNA with cytosines and amplifies the previously unmethylated DNA and the other set recognises DNA with uracil or thymine to amplify methylated targets.
  • the relative proportions of the two amplifications can be used to obtain information about the extent of methylation.
  • Chlamydia trachomatis contains genetic information on both a chromosome and a plasmid.
  • the plasmid of Chlamydia trachomatis contains 8 open reading frames and because it is present in multiple copy number it is a favoured target for NAAT detection methods of the prior art.
  • the inventors realised that many of those open reading frames contain a great deal of variability.
  • At the very least single nucleotide polymorphisms (SNPs) were detected in open reading frames 2, 4, 7 and 8.
  • Open reading frames 1 and 3 have been shown to contain both insertions and deletions.
  • the target sequence for nucleic acid detection in accordance with the invention should come from the chromosomal sequence of Chlamydia trachomatis .
  • the putative gene identified in SEQ ID NO:1, referred to herein as chromosomal sequence 17 and found on the chromosome of Chlamydia trachomatis was found to be most suitable for use in methods of the invention because it has low variability among Chlamydia trachomatis isolates, has low level of homology with non- Chlamydia trachomatis isolates and can surprisingly be detected by a PCR assay having an advantageous limit of detection (LOD) at least as good as plasmid targets despite its single copy number.
  • LOD limit of detection
  • Chromosomal sequence 17 has been suggested to be a hypothetical membrane-associated protein but has yet to be given an official name. Its function in the organism is not important in so far as its proven suitability for use in accordance with the present invention is concerned.
  • a method of detecting in a sample genetic material derived from Chlamydia trachomatis comprising sequence-specific detection of a nucleic acid sequence comprising at least 10 contiguous nucleic acid residues claimed in SEQ ID NO: 1
  • the nucleic acid sequence comprises at least 15 contiguous nucleic acid residues from SEQ ID NO: 1.
  • deletions of residues there may be 1, 2, 3 or 4 deletions of residues, substitutions of residues or additions of residues. According to certain preferred embodiments substitutions of residues are preferred over deletions of residues or additions of residues. According to certain preferred embodiments there are no substitutions, deletions or additions of residues. Similar preferred features in respect of further mutations apply to all other aspects of the invention.
  • sequence-specific detection comprises carrying out a nucleic acid hybridisation step.
  • sequence-specific detection comprises carrying out a nucleic acid hybridisation step followed by a step for detecting nucleic acid hybridisation.
  • Methods of detecting nucleic acid hybridization include methods of detecting nucleic acid hybridization in a non-sequence specific manner. These methods include the use of a nucleic acid intercalating dye, for example, ethidium bromide or SYBR-Green. These dyes increase their fluorescent signal when bound to double-stranded nucleic acid and may be detected by a standard fluorescence detection system.
  • the method of detecting nucleic acid hybridization may be a sequence-specific method, for example, labelled probes. One or more labelled probes may be hybridized to the target sequence in a sequence specific fashion or the target's sequence may be detected following hybridization to an immobilised complementary sequence (for example, on a DNA array or “chip”). Nucleic acid probes may be labelled fluorescently, radioactively, enzymatically or according to certain preferred embodiments of the invention, electrochemically. Electrochemical labelling using the electrochemical labels disclosed in this document is particularly preferred.
  • the method of detecting in a sample genetic material deriving from Chlamydia trachomatis comprises hybridization of genetic material deriving from Chlamydia trachomatis to a nucleic acid sequence comprising at least 15 contiguous nucleic acid residues containing SEQ ID NO: 4
  • the method comprises hybridization of genetic material deriving from Chlamydia trachomatis to a nucleic acid sequence comprising the sequence in SEQ ID NO: 5
  • the sequence-specific detection follows amplification of the nucleic acid to be detected using PCR, transcription-mediated amplification, nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification, recombinase polymerase amplification, strand displacement amplification or loop-mediated isothermal amplification.
  • PCR transcription-mediated amplification
  • NASBA nucleic acid sequence-based amplification
  • helicase-dependent amplification helicase-dependent amplification
  • recombinase polymerase amplification recombinase polymerase amplification
  • strand displacement amplification strand displacement amplification
  • loop-mediated isothermal amplification By using a detection method wherein sequence specific detection follows amplification of the nucleic acid to be detected, greater sensitivities and specificities in the detection method may be obtained.
  • sequence specific detection method follows amplification of the nucleic acid to be detected—that amplification being by use of a PCR.
  • Polymerase chain reaction involves the use of a forward PCR primer and a reverse PCR primer.
  • said polymerase chain reaction involves use of a forward PCR primer and a reverse PCR primer wherein:
  • SEQ ID NO: 16 aaggaagatt ccagaggcaa tgccaaagaa aaaagt
  • said polymerase chain reaction may involve use of a forward PCR primer and a reverse PCR primer wherein:
  • SEQ ID NO: 2 ttggacacta gtcagcatca agctaggaga tt;
  • SEQ ID NO: 3 gaagattcca gaggcaatgc caaagaaaaa; or wherein said forward PCR primer comprises a nucleic acid sequence that is the complement of the reverse primer as defined in part b) above and said reverse PCR primer comprises a nucleic acid sequence that is the complement of the forward primer as defined in part a) above; wherein the sequences may be further mutated by up to 5 additions of residues, deletions of residues or substitutions of residues.
  • the forward PCR primer may be as defined with respect to the second aspect of the invention and the reverse PCR primer may be as defined with respect to the third aspect of the invention.
  • the forward PCR primer comprises a nucleic acid having the sequence given in SEQ ID NO: 17, SEQ ID NO: 18 or SEQ ID NO: 6
  • SEQ ID NO: 6 cactagtcag catcaagcta gg
  • SEQ ID NO: 17 caaacctcac tagtcagcat caagctagg
  • SEQ ID NO: 18 gtttggacac tagtcagcat caagctagg
  • the reverse PCR primer comprises a nucleic acid having the sequence given in SEQ ID NO: 19 or SEQ ID NO: 7
  • SEQ ID NO: 7 ttccagaggc aatgccaaag
  • SEQ ID NO: 19 agattccaga ggcaatgcca aagaaa
  • the PCR primers may be labelled to assist detection of hybridization.
  • the label may be a fluorescence label, a radioactive label, an enzymatically active label or an electrochemically active label.
  • the primer and label may be arranged such that their detectable signal increases following hybridization or following degradation by the exonuclease activity of the DNA polymerase used in the PCR reaction.
  • the label may be applied to a PCR primer to which a quencher moiety has also been added. Degradation of the PCR primer will result in the quencher moiety and the label becoming separated from each other and the quenching activity of the quencher on the label becoming diminished.
  • a nucleic acid probe may be used to detect in a sequence-specific fashion the products of a PCR reaction. Typically, such a probe is designed to anneal to the target sequence at a position intermediate between the positions at which the primers anneal.
  • the probe may be labelled to assist in its detection, for example, a fluorophore, a radioactive label, an electrochemically active label or an enzymatic label.
  • the label may be linked directly to the nucleic acid or by means of a linker moiety.
  • the probes of the present invention are particularly suitable for the TaqMan PCR format. TaqMan is a method of real time quantitative PCR available from Life Technologies Inc.
  • telomere length a segment of approximately 20 to 60 nucleotides within the DNA template located between the two primers.
  • Suitable fluorescent labels for use in a TaqMan system include 6 carboxy-fluorescein (FAM) or tetrachlorofluorescein (TET).
  • the TaqMan probe is typically labelled with such a fluorophore and also labelled with a quencher molecule, for example, tetramethylrhodamine (TAMRA).
  • TAMRA tetramethylrhodamine
  • the close proximity between the fluorophore and the quencher inhibits the fluorescence of the fluorochrome.
  • the Taq polymerase also exhibits 5′ to 3′ exonuclease activity which degrades the portion of the probe that is already annealed to the template. Degradation of the probe releases fluorochrome from it.
  • the fluorochrome is no longer in close proximity to the quencher, thus the quenching effect is diminished and the fluorescent signal given off by the fluorochrome increases and may be detected.
  • the polymerase chain reaction involves the use of a nucleic acid probe comprising a nucleic acid sequence.
  • Said nucleic acid sequence comprising between 18 and 28 nucleic acid residues given in SEQ ID NO: 4
  • the nucleic acid sequence comprises between 19 and 27 nucleic acid residues given in SEQ ID NO: 4, more preferably between 20 and 26 nucleic acid residues, more preferably between 21 and 25 nucleic acid residues, more preferably, between 22 and 24 nucleic acid residues, most preferably 23 nucleic acid residues.
  • the nucleic acid probe comprises a nucleic acid sequence given in SEQ ID NO: 5
  • the nucleic acid probe may be labelled, for example, fluorescently, radioactively, enzymatically or most preferably with an electrochemically active label.
  • electrochemically active labels disclosed therein are especially preferred.
  • a forward PCR primer comprising a nucleic acid sequence comprising between 17 and 34 (for example, 24 and 34) contiguous nucleotide resides selected from SEQ ID NO: 15;
  • SEQ ID NO: 15 tgatg - g/c-t/a-t/a-t/a-g/c -g/c-a/t- cactagtc agcatcaagc taggagatt
  • a forward PCR primer comprising a nucleic acid sequence comprising between 17 and 27 contiguous nucleotide residues selected from SEQ ID NO: 2;
  • SEQ ID NO: 2 ttggacacta gtcagcatca agctaggaga tt;
  • a forward PCR primer comprising a nucleic acid sequence comprising between 24 and 34 contiguous nucleotide residues selected from SEQ ID NO: 20;
  • SEQ ID NO: 20 tgatgcaaac ctcactagtc agcatcaagc taggagatt;
  • a forward PCR primer comprising a nucleic acid sequence comprising between 24 and 24 contiguous nucleotide residues selected from SEQ ID NO: 21;
  • SEQ ID NO: 21 tgatggtttg gacactagtc agcatcaagc tagg agatt;
  • the nucleic acid sequence comprises between 18 and 26, between 19 and 25, between 20 and 24, between 21 and 23, most preferably 22 residues or between 25 and 33, between 26 and 32, between 27 and 31, between 28 and 30 most preferably 29 residues.
  • the forward PCR primer comprises a nucleic acid having sequence given in SEQ ID NO: 17, SEQ ID NO: 18 or SEQ ID NO: 6.
  • SEQ ID NO: 6 cactagtcag catcaagcta gg
  • SEQ ID NO: 17 caaacctcac tagtcagcat caagctagg
  • SEQ ID NO: 18 gtttggacac tagtcagcat caagctagg.
  • a reverse PCR primer comprising a nucleic acid sequence comprising a nucleic acid sequence comprising between 15 and 31 (for example between 21 and 31) contiguous nucleotide residues selected from SEQ ID NO: 16;
  • SEQ ID NO: 16 aaggaagatt ccagaggcaa tgccaaagaa aaaagt;
  • a reverse PCR primer comprising a nucleic acid sequence comprising between 15 and 25 contiguous nucleotide residues selected from SEQ NO: 3
  • SEQ ID NO: 3 gaagattcca gaggcaatgc caaagaaaaa;
  • the nucleic acid sequence comprises between 22 and 30 contiguous nucleotide residues selected from SEQ ID NO: 16. More preferably between 23 and 29, more preferably between 24 and 28, more preferably between 25 and 27, most preferable 26 residues.
  • the nucleic acid sequence comprises between 16 and 24 contiguous nucleotide residues selected from SEQ ID NO: 3. More preferably between 17 and 23 more preferably between 18 and 22, more preferably between 19 and 21, most preferably 20 residues.
  • the numbers and types of additions, deletions and substitutions of residues may be as defined above in reference to the forward PCR primer.
  • the reverse PCR primer comprises a nucleic acid sequence given in SEQ ID NO: 19 or SEQ ID NO: 7
  • SEQ ID NO: 7 ttccagaggc aatgcdaaag
  • SEQ ID NO: 19 agattccaga ggcaatgcca aagaaa
  • nucleic acid probe comprising a nucleic acid sequence, said nucleic acid sequence comprising between 18 and 28 nucleic acid residues given in SEQ ID NO: 4
  • the number and type of additions, deletions, substitutions of residues may be as defined above in reference to the primers of the invention.
  • the nucleic acid probe according to certain preferred embodiments comprises between 18 and 27, between 19 and 26, between 20 and 25, between 21 and 24, between 22 and 23, most preferably 23 residues from SEQ ID NO: 4.
  • a nucleic acid probe of the invention comprises a nucleic acid sequence given in SEQ ID NO: 5
  • SEQ ID NO: 5 ctgtccgctg gttcttcctt act.
  • a PCR component comprising a forward PCR primer of the invention and a reverse PCR primer according to the invention.
  • the PCR component further comprises a nucleic acid probe according to the invention.
  • assay internal controls for a PCR or similar assay consist of single-stranded DNA oligonucleotides. These can be simply manufactured and immobilised onto a sample carrier or added to a component of the PCR reaction. However, the methods of the present invention may be preceded by sample preparation steps which may involved purifying elementary bodies or clinically derived Chlamydia -containing material and purifying genomic DNA from them. A number of commercially available DNA purification methods and kits are available, for example, the Promega Wizard System. These bacterial lysis and DNA Purification systems involve the use of a chaotropic salt containing solution with DNA binding to a membrane, for example, a silica-based membrane followed by the removal of the remaining lysate and washing to remove contaminants.
  • the purified bacterial genomic DNA is then recovered from the membrane for use in the downstream detection assay, for example, an assay in accordance with the first aspect of the present invention.
  • Such purification methods are unlikely to co-purify short single-stranded DNA, oligonucleotide based internal control sequences.
  • the Promega Wizard kit states that their purification protocol has a 50 kb size cut off. The inventor therefore realises that it would be advantageous to provide an internal control which would co-purify with the Chlamydia genomic DNA contained in the sample.
  • a possible solution is to use as an internal control a genomic DNA from another bacterial species using the same lysis in isolation conditions required to isolate genomic DNA from Chlamydia .
  • the source of the internal control should ideally be derived from a non-pathogenic bacterium. Also it should be not normally be readily found in humans and should be easily culturable in a laboratory.
  • the present invention involves the use of genomic DNA as in internal control which has been derived from Pectobacterium atrosepticum. This is because P. atrosepticum is culturable, widely-available and DNA isolated from it is easily co-purified with that derived from Chlamydia . It has only one chromosome and possesses many genes which appear unique to the species.
  • the PCR component further comprises genomic DNA derived from Pectobacterium atrosepticium for use as an internal positive control.
  • it is of the strain ATCC BAA-672.
  • a PCR component according to the invention preferably comprise a second forward PCR primer and a second reverse PCR primer wherein said primers are designed to hybridize to nucleic acid sequences found within a nucleic acid sequence of SEQ ID NO: 8
  • the second forward PCR primer preferably comprises a nucleic acid sequence, comprising between 13 and 23 contiguous nucleic acid residues selected from SEQ ID NO: 9
  • SEQ ID NO: 9 ctcgctgtcg ggaagtttgg ttgaaccg;
  • the second reverse PCR primer preferably comprises a nucleic acid sequence comprising between 15 and 25 contiguous nucleic acid residues selected from SEQ ID NO: 10
  • SEQ ID NO: 10 acaggcctga actgggaatc ctttgatttc;
  • said second forward PCR primer comprises a nucleic acid sequence that is a complement of the reverse primer as defined above and said second reverse PCR primer comprises a nucleic acid sequence that is the complement of the forward primer as defined above; wherein the sequences may be further mutated by up to 5 additions of residues, deletions of residues or substitutions of residues as defined in number and type above in reference to primers in accordance with the first or second aspect of the invention.
  • the second forward PCR primer preferably comprises between 14 and 22 contiguous nucleic acid residues selected from SEQ ID NO: 9, more preferably between 15 and 21, more preferably between 16 and 20, more preferably between 17 and 19; most preferably 18 contiguous nucleic acid residues selected from SEQ ID NO: 9.
  • the second reverse PCR primer preferably comprises between 16 and 24 contiguous nucleic acid residues selected from SEQ ID NO: 10, most preferably between 17 and 23, more preferably between 18 and 22, more preferably between 19 and 21, most preferably 20 contiguous nucleic acid sequences selected from SEQ ID NO: 10.
  • the second forward PCR primer comprises a nucleic acid sequence as given in SEQ ID NO: 11
  • SEQ ID NO: 12 cctgaactgg gaatcctttgg
  • the PCR component contains a second nucleic acid probe comprising a nucleic acid sequence, said nucleic acid sequence comprising between 18 and 28, more preferably between 19 and 27, more preferably between 20 and 26, more preferably between 21 and 25, more preferably between 22 and 24, most preferably 23 nucleic acid residues given in SEQ ID NO: 13
  • SEQ ID NO: 13 ggagagcacg atccctttcc taaagacgtt acc
  • the nucleic acid probe comprises a nucleic acid sequence given in SEQ ID NO: 14
  • SEQ ID NO: 14 gcacgatccc tttcctaaag acg
  • the present invention also contemplates products and methods relating to an internal control comprising Pectobacterium atrosepticum in the absence of products and methods for detection of Chlamydia trachomatis (ie for use as an internal control for the detection of nucleic acids other than those from Chlamydia trachomatis ).
  • the invention contemplates a forward PCR primer and further contemplates a second PCR primer wherein said primers are designed to hybridise to a target nucleic acid sequence found within the genomic DNA of Pectobacterium atrosepticum .
  • the primers are designed to hybridise the target nucleic acid sequence found within the nucleic acid sequence SEQ ID NO: 8
  • the invention also contemplates a nucleic acid probe for detection of the Pectobacterium atrosepticum internal positive control having features as defined in reference to other aspects of the invention.
  • the invention also contemplates a method of detecting a signal from an internal positive control comprising Pectobacterium atrosepticum comprising use of Pectobacterium atrosepticum primers, an optional probe and incorporating any of the features disclosed herein in reference to other methods of the invention.
  • a method of detecting the signal from an internal positive control comprising Pectobacterium atrosepticum preferably is preceded by a method of obtaining genomic DNA from Pectobacterium atrosepticum comprising lysis of whole Pectobacterium atrosepticum bacterial cells using chaotropic salts and optionally a silica-based membrane as described herein.
  • kits comprising a PCR component according to the fifth aspect of the invention or a PCR primer or probe according to eighth, ninth or tenth and instructions for carrying out a method according to the first aspect of the invention.
  • a kit may contain further components for example sample vessels, packaging, PCR enzymes, amplification pre-cursors, sample tubes or detection instruments;
  • a PCR component of the fifth aspect of the invention further comprises genomic DNA derived from Pectobacterium atrosepticium for use as an internal positive control.
  • the method of detection may be as described herein in reference to other aspects of the invention or may involve using compounds or products described herein in reference to other aspects of the invention.
  • a method of detecting in a sample genetic material deriving from Pectobacterium atrosepticium comprising sequence-specific detection of a nucleic acid sequence, contained in the chromosome of Pectobacterium atrosepticium .
  • Said method may incorporate any feature disclosed in relation to other aspects of the invention and may optionally further comprise the extraction of genomic DNA from a sample said genomic DNA being that of Pectobacterium atrosepticium (optionally introduced to the sample as an internal control).
  • Said extraction may be concomitant with the extraction of genomic DNA from a second organism (for example a bacterial pathogen) of interest.
  • forward PCR primers as defined as a “second forward PCR primer” in accordance with the fifth aspect of the invention
  • reverse PCR primer as defined as a “second reverse PCR primer” in accordance with the fifth aspect of the invention
  • PCR probe as defined as a “second PCR probe” in accordance with the fifth aspect of the invention.
  • the invention also provides PCR components comprising any one or more forward PCR primer, reverse PCR primer or PCR probe in accordance with the eighth, ninth or tenth aspect of the invention in combination with one or more further components of a PCR reaction.
  • the probes and/or primers may be linked to a label to assist their detection. That label may be radioactive, enzymatically active, fluorescently active or electrochemically active. According to embodiments Wherein there are components for the detection of nucleic acid deriving from Chlamydia trachomatis and also components for the detection of nucleic acids deriving from the internal positive control or wherein there is a method of simultaneous detection of the two nucleic acids, the labels used to assist in the detection of the internal positive control and in the detection of nucleic acid deriving from Chlamydia trachomatis are preferably distinguishable from each other, for example, they may be different fluorochromes or they may be different electrochemically active agents or electrochemically active labels providing electrochemically distinguishable activity.
  • the present invention is especially suitable for use with electrochemically labelled probes and/or primers.
  • the electrochemical label may include those comprising metallo-carbocyclic pi complexes, that is organic complexes with partially or fully delocalized pi electrons.
  • Suitable markers include those comprising sandwich compounds in which two carbocyclic rings are parallel, and also bent sandwiches (angular compounds) and monocyclopentadienyls.
  • the electrochemically active markers are metallocenyl labels. More preferably they are ferrocenyl labels.
  • Ferrocenyl and metallocenyl labels used in the probes according to the invention may advantageously be N-substituted ferrocene or metallocene carboxamides.
  • the ferrocene or metallocene ring, which constitutes the labelling moiety, may be unsubstituted.
  • the ferrocene or metallocene ring may be substituted by one or more substituents, the nature and location of which are selected so as to influence in a desired manner the redox characteristics of the ferrocene or metallocene moiety.
  • the ferrocene or metallocene ring may additionally or instead be substituted by any ring substituents that do not materially reduce the electrochemical sensitivity of the label.
  • the ferrocene or metallocene carboxamide moiety may be linked via the carboxamide nitrogen to the nucleotide or oligonucleotide.
  • Linkage to the nucleotide or oligonucleotide is preferably via a phosphate group or via the base of the nucleotide. Both methods of linkage permit the label to be attached via any nucleotide along the length of the oligonucleotide. However if linkage is via a phosphate group it is advantageously via a 3′ or 5′ terminal phosphate group so as to minimise the likelihood that such linkage will sterically hinder Watson-Crick hybridization of the oligonucleotide or affect nuclease activity.
  • Linkage via a region of the base not involved in Watson-Crick base pairing is predicted to be less disruptive of such base pairing. Therefore linkage via the base may be more suitable for labelling at non-terminal oligonucleotide sites.
  • the label oligonucleotide may have a linker moiety between the oligonucleotide and the labelling moiety.
  • the labelled oligonucleotides have a ferrocenyl labelling moiety which is linked to the oligonucleotide by a linker moiety.
  • Suitable linker moieties may comprise an aliphatic chain which may be linear or branched, and saturated or unsaturated.
  • the linker moiety is a linear or branched aliphatic chain having from 4 to 20 carbon atoms, and preferably from 6 to 16, especially from 8 to 14 atoms, especially 12 carbon atoms.
  • the alkylene chains may be substituted by any substituent or may be interrupted by any atom or moiety provided that any such substituent, atom or moiety does not materially reduce the electrochemical sensitivity of the label.
  • Illustrative, of the ferrocenyl labels which may be used in accordance with the invention are those in Formulae I to III.
  • Molecules of formula Ia to IIIa are oligonucleotides labelled with the corresponding ferrocenyl labels.
  • Formula IV is illustrative of a ferrocenyl label which may be attached via a nucleotide base, the amino-modified thymine base being included in Formula IV for the purposes of illustration.
  • the ferrocene labelled probes may be made by any suitable method.
  • the oligonucleotide may be an oligonucleotide modified by introduction of a radical having a terminal amino group.
  • Illustrative of such amino-modified nucleotides is the modified nucleotide of Formula V.
  • the ferrocene may then be incorporated by reaction of the amino-modified nucleotide with the N-hydroxy-succinimide ester of ferrocene carboxylic acid (Formula VI) to obtain ferrocene labelled oligonucleotide.
  • ferrocene labelled oligonucleotides may be prepared by addition of the ferrocene moiety during solid phase oligonucleotide synthesis.
  • Ferrocene labels can be introduced into an oligonucleotide during solid phase synthesis by two general methods: Firstly, addition of the olignucleotide at the 3′ end of the oligonucleotide requires the use of a suitable resin. Such a resin is labelled with a ferrocene derivative.
  • ferrocene at an internal site, or at the 5′ end of an oligonucleotide requires the use of a coupling reagent suitable for coupling with a solid support bound oligonucleotide, for example a ferrocenyl derivative phosphoramidite, for example as shown as formula IX or X.
  • a coupling reagent suitable for coupling with a solid support bound oligonucleotide for example a ferrocenyl derivative phosphoramidite, for example as shown as formula IX or X.
  • the electrochemically active label may be a compound of: Mc-NR′—C( ⁇ O)—X—(Ar) n -(L) m -R XI Wherein
  • the Mc group may be substituted by one or more groups selected lower alkyl (for example C1 to C4 alkyl), lower alkyl substituted with a hydroxy, halo, cyano, oxo, amino, ester amido or a further metallocene group, lower alkenyl, lower alkenyl substituted with a hydroxy, halo; cyano, oxo, amino, ester, amido or a further metallocene group, aryl, aryl substituted with a hydroxy, halo; cyano, oxo; amino, ester, amido or a further metallocene group.
  • the further metallocene group may be substituted in the same way as the Mc group with the exception that the total number Mc groups in the molecule of the invention preferably does not exceed four.
  • the Mc group is unsubstituted.
  • M is an ion selected from iron, osmium or ruthenium. Most preferably, M is an iron ion. When M is an iron ion, Mc is a ferrocene.
  • Lower alkyl is preferably C1 to C4 alkyl.
  • R′ is H.
  • Each R′ has an identity separate from the other R′.
  • X is NH
  • the Ar group may be substituted by one or more groups selected lower alkyl (for example C 1 to C 4 alkyl), lower alkyl substituted with a hydroxy, halo, cyano, oxo, amino, ester or amido group, lower alkenyl, lower alkenyl substituted with a hydroxy, halo, cyano, oxo, amino, ester or amido group, aryl or aryl substituted with a hydroxy, halo, cyano, oxo, amino, ester or amido group.
  • the Ar group is unsubstituted.
  • n 1.
  • m 1.
  • Suitable linker groups L may comprise an aliphatic chain which may be linear or branched, and saturated or unsaturated.
  • the linker moiety is a linear or branched aliphatic chain having from 4 to 20 carbon atoms, and preferably from 6 to 16, especially from 8 to 14 atoms, more especially 12 carbon atoms.
  • the alkylene chains may be substituted by any substituent or may be interrupted by any atom or moiety provided that any such substituent, atom or moiety does not materially reduce the electrochemical sensitivity of the label.
  • the compound of the invention may comprise more than one metallocene groups.
  • the metallocene group may be substituted by any other electrochemically active marker group.
  • the compound may be one which is electrochemically active or becomes electrochemically active following partial cleavage.
  • the moiety to be labelled is an amino acid, a nucleotide, an oligonucleotide, a polynucleotide, a nucleoside, a sugar, a carbohydrate, a peptide, a protein or a derivative of any of those molecules.
  • R is a nucleotide or an oligonucleotide.
  • the nucleotide may be selected from adenosine, thymidine, guanosine, cytidine, or uridine.
  • the nucleotide is attached through a group attached to the ribose or deoxyribose group of the nucleotide, for example in the 2′, 3′ or 5′ position. Most preferably, the nucleotide is attached at the 3′ or 5′ position, for example at the 5′ position. Preferably, the attachment at the 2′, 3′′ or 5′ position is through an oxygen or a nitrogen atom.
  • the labeling reagent may be attached directly or via a linker.
  • the linker may be attached first to the labeling reagent or to the molecule to be labelled. If the linker is first attached to the Molecule to be labelled it may comprise a group, for example, an amino or a thiol group, that will assist in the labeling reaction. An amino group is preferred.
  • the nucleotide or an oligonucleotide is preferably labelled, to the 3′ or 5′ end.
  • the oligonucleotide may be amino-modified to assist with the labeling reaction.
  • Amino-modified oligonucleotides may be synthesized by standard techniques and are available from a wide range of commercial sources for example from Oswel Scientific (Southampton, UK).
  • the amino-modified oligonucleotide may also incorporate a linker motif, for example, the modification may be the addition of 5′ aminohexyl or 3′ aminohexyl or a 5′-C12 amino-group.
  • a labelled molecule of interest preferably comprises a linker.
  • the sequence of the oligonucleotide portion of the molecule is preferably such that the molecule is able to hybridize with a complementary target sequence and thus be used as a probe in a molecular biological technique, for example, one of the nucleic acid detection or qualification techniques disclosed in this specification.
  • Labelled biological molecules in accordance with the invention may be electrochemically active in either digested or non-digested states. Ideally the extent of electrochemical activity will vary in dependence on the extent of digestion.
  • Formula VIII illustrates a possible mode of attachment of the novel electrochemically active marker to an oligonucleotide.
  • the molecule of formula VIII may be obtained by reacting a 5′-aminohexyl modified oligonucleotide with the molecule shown in formula VII.
  • N-hydroxysuccinimide ester of 4-(3′-ferrocenylureido)-1-benzoic acid Details of the use of said compound to label oligonucleotides are provided in Examples 7 and 8. It will however be apparent to the skilled person that such a label may be attached to an oligonucleotide at any suitable position and that attachment is not limited to the 5′ end of said oligonucleotide.
  • EP1481 083 which is hereby incorporated by reference.
  • primers and probes may be shorter than those specified above particularly if steps are taken to increase the annealing temperature of the primer (and the Applicant specifically contemplates lengths of 1, 2, 3, 4 or 5 nucleotide residues shorter than the lengths and ranges specifically disclosed above).
  • shorter primer and probes may be facilitated by the use of minor groove binder moieties and also lock nucleic acids (also known as locked nucleic acids or LNAs) which increase thermal stability of primers and probes and increase the annealing temperature of the primer or probe.
  • LNAs locked nucleic acids
  • the present invention in all its aspects contemplates use of shorter primer and probes wherein increased thermal stability is facilitated by the use of minor groove binder moieties and/or lock nucleic acids in combination with primers and probes described herein which do not have increased thermal stability as facilitated by the use of minor groove binder moieties and/or lock nucleic acids as well as exclusive use of primers and probes having increased thermal stability as facilitated by the use of minor groove binder moieties and/or lock nucleic acids.
  • LNAs Locked Nucleic Acids
  • An LNA is a nucleic acid incorporating one or more modified RNA or DNA nucleotide residues (in combination with ordinary DNA or RNA residues).
  • an extra covalent bridge connects the 2′ and 3′ carbons and “locks” the ribose sugar in the 3′—endo structural conformation as normally found in the A-form of RNA and DNA.
  • LNA includes all nucleic acids incorporating locked residues at some or all residue positions.
  • the lock may be achieved by any chemical bridge connecting the 2′ and 3′ carbons of the sugar moiety.
  • Preferably the lock is achieved in a 2′-0, 4′-C methylene linkage.
  • LNAs display increased thermal stability, with melting temperature rising by about 5° C. compare to corresponding DNA or RNA oligomers. Because of the elevated melting temperature, the risk of LNA primers and probes forming hairpin structures detrimental to efficient PCR reactions is increased. Good primer and probe design therefore becomes even more essential and in relation to the present application LNA primers and probes corresponding to those disclosed in SEQ ID NOS: 5, 6, 7, 11, 12 and 14, optionally shortened by 1, 2, 3, 4 or 5 residues from either end, are especially preferred.
  • LNAs can be readily prepared and are commercially available from a number of suppliers.
  • the invention also relates to nucleic acid probes and primers (including LNA probes and primers) conjugated to minor groove binder (MGB) moieties.
  • MGB minor groove binder
  • MGB moieties are isometrical-shaped groups which bind in the minor groove of a double helix forming between the probe or primer and target. They stabilize the double stranded region and increase the melting temperature and specificity of the probe/primer, allowing shorter probes/primers to be used.
  • MGB moieties and methods of attachment the reader is referred to Katyavin et al. (2000) Nucleic Acid Res. 28(2):655-661 and references therein which are hereby incorporated by reference.
  • Minor groove binding moieties may be readily prepared and attached to primers and probes and are commercially available from a number of suppliers.
  • samples may include clinical samples, including tissues and fluids not limited to blood, plasma, serum, secretions, semen, seminal plasma; tears and saliva.
  • sample also includes derivatives of clinical samples, for example, samples which have been filtered, clotted, disinfected, irradiated or separated, and also used medical devices or dressings previously in contact with a subject. Said subject is preferably human.
  • Primer sets were obtained for plasmid amplicons 1, 3, 4, 5, 6, 7 and 8. To screen these primer sets, symmetric PCR reactions using 10,000 EBs per reaction, were set up in triplicate for each primer set according to table 1 below.
  • Primer sets were obtained for amplicons numbers 1, 5, 9, 17 and 18. To screen these primer sets, symmetric PCR reactions using 10,000 EBs per reaction were set up in triplicate for each primer set according to table 1 above. Negative reactions were included in triplicate for each primer set. PCR reaction conditions were as described above.
  • Negative reactions were included in triplicate for each primer set. PCR reaction conditions were as stated above in Example 1.
  • Negative values obtained were “no peak” negatives. Triplicate one-copy positives were recorded for plasmid amplicons 3 and 7, however only one positive value out of three was recorded for plasmid amplicon 5. Therefore, plasmid amplicon 5 was eliminated at this stage and the experiment for plasmid amplicons 3 and 7 repeated, again in triplicate as above. These results were highly similar to that obtained above.
  • plasmid amplicon 7 showed sustained peak heights and appeared the best to use as a plasmid primer set
  • an exclusivity experiment using asymmetric PCR, T7 exonuclease digestion and electrochemical detection was carried out using Chlamydophila pneumoniae .
  • Primer and probe set for plasmid amplicon 3 did not show this positive signal, and was therefore selected as the leading candidate for detection of the Chlamydia trachomatis plasmid.
  • MgCl 2 concentration of MgCl 2 .
  • This experiment was completed with final MgCl 2 concentrations per reaction of 2.0 mM to 5.0 mM in 0.5 mM increments using 10,000 EBs per asymmetric PCR, followed by probe addition, T7 digestion and electrochemical measurement. The data obtained suggested that a final MgCl 2 concentration of 5.0 in M allowed the greatest peak height to be obtained under the conditions tested.
  • the data shows that running PCRs using 5.0 mM MgCl 2 gives optimal performance when 1,000 EBs are used per reaction compared to 10,000 or 100,000 EBs per reaction. Following the 1,000 EB level, the peak heights fall to a mean value at 1 EB of 54.97 nA.
  • the chromosomal amplicon 17 (SEQ ID NO: 1) primer and probe set was selected as the leading candidate for Chlamydia trachomatis chromosomal target detection.
  • the forward and reverse primer and probe sequences are respectively as given in SEQ ID NOS: 6, 7 and 5.
  • Chlamydia assay is highly specific to Chlamydia trachomatis only and that no cross-reactivity is apparent across other species of bacteria or any other organisms.
  • primer and probe design phase outlined in Examples 1 to 3, it was shown that bioinformatically there was no cross-reactivity, however it was essential to demonstrate this, experimentally using real microbial isolates.
  • the assay was able to detect all 15 genital serovars of Chlamydia trachomatis and to know which other serovars (that cause ocular or arthritic disease) are also able to be amplified by the assay primer set.
  • DNA samples derived from a panel of bacteria were tested against both the plasmid and genomic primers to test for specificity (exclusivity) using PCR and probe-T7 endpoint detection.
  • Chlamydia trachomatis serovars were then obtained (as EBs) and the DNA extracted, purified and quantified. Three levels of copies of DNA were then tested using both the plasmid and genomic primer sets followed by probe-T7 exonuclease endpoint detection to establish if all serovars had similar LoDs.
  • Genomic primer sets were tested in duplicate against the list of DNA as specified in the introduction. Output was measured in signal peak height following PCR, and probe-T7 detection. Testing was carried out in batches with PCR controls for each batch tested.
  • EBs obtained for all 15 C. trachomatis serotypes (A, B, Ba, C, D, E, F, G, H, I, J, K, L1, L2, L3) were lysed and their DNA purified and quantified. Levels of 50,000, 500, 50 or 5 genome copies of each serotype were tested for inclusivity in PCR reactions using primers and probes as outlined above (SEQ ID NOS: 6 and 7 and 5). Signal peak height was measured after endpoint detection using probe-T7.
  • the 5.064 Mb Pectobacterium atrospeticum genome (accession No. BX950851) was downloaded from the NCBI Pubmed website.
  • the Pectobacterium atrosepticum genome is fully annotated with gene names, functions and genomic location, including hypothetical genes. Three genes were selected for investigation.
  • rfaH (starting at base pair position 230144 of 489 bp in length running in the reverse orientation which encodes a transcriptional activator protein)
  • mgsA (starting at base pair position 2008746 of 458 bp in length running in the reverse orientation which encodes a methylgloxal synthase)
  • HP1 a gene encoding a hypothetical protein, designated HP1, starting at base pair position 143610 of 387 bp in length running in the reverse orientation.
  • the full-length gene sequences were selected from the genome using the Clone Manager program.
  • the primer design function of the program was used to choose primer sets of optimal length 20 bases (18-22 bases acceptable), amplifying a product of between 90 and 150 bp from each gene.
  • the criteria applied for each primer were to have a GC % of between 50-60%, a Tm of 50-80° C., with less than 3 matches at the 3′ end, less than 7 adjacent homologous bases, stability greater than or equal to 1.2 kcal at the 5′ end vs the 3′ end, at least one G or C at the 3′ end, less than four base runs, less than three dinucleotide repeats and no hairpins with annealing temperatures of 55° C.
  • the three primer sets were tested using PCR with Pectobacterium atrospeticum strain SCRI1043 genomic DNA corresponding to ATCC bacterial deposit having accession number BAA-672. Symmetric PCR was carried out using the reaction conditions shown in the table below and cycling conditions as shown in table 4 and table 5 below.
  • Electrochemical probes were synthesised using ferrocene labels for each of the three probe sequences.
  • Two nanograms of Pectobacterium atrospeticum genomic DNA was amplified in triplicate reactions using the rfaH, mgsA and HP 1 primer sets under symmetric PCR conditions (shown in table 5, above) or asymmetric PCR conditions using the reaction conditions shown in table 6 (below), both with the cycling conditions shown in table 5 above.
  • Triplicate negative (water-only) controls were run in triplicate for each primer set for each amplification condition.
  • the data shown in Table 8 clearly indicate that the peak heights obtained using the HP1 probe was higher than all others tested with mean peak heights of 611.33 nA being obtained. Along with mean negative peak heights of 53.7, this would allow the greatest possible discrimination between positive and negative signals.
  • the peak locations for asymmetric conditions for positive HP1 samples were identical, and asymmetric conditions for negative HP1 samples gave low standard deviation and coefficient of variation.
  • the mgsA amplicon/probe set allowed poor discrimination and the rfaH ampicon/probe set gave good discrimination, however this was not of the order seen with the HP1 set. Therefore, the HP1 primer/probe set was chosen for internal control purposes.
  • the chosen forward primer corresponds to SEQ ID NO: 11.
  • the chosen reverse primer corresponds to SEQ ID NO: 12.
  • the chosen probe corresponds to SEQ ID NO: 14.
  • DNA samples derived from a panel of bacteria were tested against the internal control primers (SEQ ID NOS: 11 and 12) to test for specificity (exclusivity) using PCR and probe-T7 exonuclease endpoint detection, with probe sequence as in SEQ ID NO: 14.
  • Genomic primer sets were tested in duplicate against the list of DNA as specified in the results. Output was measured in signal peak height following PCR, and probe-T7 exonuclease detection. Testing was carried out in batches with PCR controls for each batch tested.
  • Peak location (milli Peak height (nano Species Volts) Amps) Acinetobacter baumanii No peak No peak No peak No peak No peak No peak Acinetobacter genospecies 9 No peak No peak No peak No peak No peak No peak No peak No peak Acinetobacter haemolyticus No peak No peak 202 26.0 Anaerococcus tetradius No peak No peak No peak No peak No peak Arcanobacterium pyogenes No peak No peak 202 30.2 Bacillus cereus 202 20.3 No peak No peak Bacteroides fragilis No peak No peak No peak No peak No peak No peak Bacteroides thetaiotamicron No peak No peak 202 35.3 Bacteroides vulgatus No peak No peak No peak No peak No peak No peak No peak No peak No peak No peak No peak Bifidobacterium breve 193 16.8 No peak No peak No peak Bordetella pertussis No peak No peak No peak No peak No peak Burkholderia cepacia
  • a PCR mastermix was made by combining the following:
  • the mastermix was divided into aliquots of 12.5 ⁇ l. DNA extracted from 1,000, 100, 10 and 0 C. trachomatis EBs was added in 12.5 ⁇ l volumes. Samples were then incubated for UDG activity and denaturation followed by PCR as described below:
  • Amplified samples were used as a target for detection in the following assay using 0.8 U T7 exonuclease and 9 ⁇ M specific probe having the sequence of SEQ ID NO: 5 (final reaction concentrations). Each sample was assayed in triplicate.
  • the detection mix was made up by combining:
  • Results are shown in FIG. 3 .
  • FIG. 4 clearly shows that the amplification of C. trachomatis in the presence of the Internal Control primer set, and not Internal Control DNA alone, adversely affects the electrochemical signal obtained for detections using the C. trachomatis probe.
  • the same experiment was carried out using the Internal Control probe to electrochemically detect internal control amplicons. The data obtained is shown in FIG. 5 .
  • FIG. 5 shows a dramatic reduction in the Internal Control electrochemical signal expected for “singlex” PCRs containing the Internal Control Primers and 200 pg chromosomal Internal Control target molecule, where peak heights in excess of 1,000 nA are commonly observed.
  • FIGS. 6 a and 6 b C. trachomatis primer sets alone
  • FIGS. 7 a and 7 b C. trachomatis and Internal Control primer sets
  • sequence similarity is hypothesized to account for the poor amplification and detection of C. trachomatis in duplex reactions containing the Internal Control reverse primer due to the formation of primer dimers during thermal cycling.
  • New CT fw primer (SEQ ID NO: 17) 5′-caaacctcac tagtcagcat caagctagg-3′
  • New CT rv primer (SEQ ID NO: 19) 5′-agattccaga ggcaatgcca aagaaa-3′
  • the seven additional base pairs that were added, on to the 5′ end of the CT forward primer were intended to be a 5′ continuation of the sequence to the strand of the C. trachomatis chromosomal DNA that the primer was designed for.
  • an error in primer design meant that these seven additional bases were in fact complementary to what was intended for inclusion. Nevertheless, this appears to have achieved the aim of bringing the T m s of each primer closer to each other, whilst retaining the performance previously observed with the “old” C. trachomatis forward primer (SEQ ID NO: 6).
  • the data shown in FIG. 8 demonstrates that the modified C. trachomatis primer set, when combined with the existing Internal Control primer set, permits co-amplification and electrochemical detection of these targets using duplex PCR.
  • Mastermix A used primers SEQ ID NOS; 6 and 7 and probe SEQ ID NO: 5 for the C. trachomatis reaction and show a limit of detection between 10,000 and 1,000 IFU.
  • Mastermix B used primers SEQ ID NOS: 17 and 19 and probe SEQ ID NO: 5 for the C. trachomatis reactions and shows a limit of detection between 10 IFU and 1 IFU.
  • Mastermix C used primers SEQ ID NOS: 18 and 19 and probe SEQ ID NO: 5 for the C. trachomatis reactions and shows a limit of detection between 10 and 1 IFU.

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Publication number Priority date Publication date Assignee Title
US10450616B1 (en) 2018-05-09 2019-10-22 Talis Biomedical Corporation Polynucleotides for the amplification and detection of Chlamydia trachomatis
US11326214B2 (en) 2018-05-09 2022-05-10 Talis Biomedical Corporation Polynucleotides for the amplification and detection of chlamydia trachomatis
US10954572B2 (en) 2019-07-25 2021-03-23 Talis Biomedical Corporation Polynucleotides for the amplification and detection of Neisseria gonorrhoeae
US11891662B2 (en) 2019-12-02 2024-02-06 Talis Biomedical Corporation Polynucleotides for amplification and detection of human beta actin

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